There is insufficient memory for the Java Runtime Environment to continue. about gor HOT 6 CLOSED

@snorristurluson you have any pointers for increasing the memory limit of the gor shell?

from gor.

That's strange, the gor shell isn't set up any different from gorpipe.

Try the following to control the memory given to the JVM:
export JAVA_OPTS=-Xms2G -Xmx5G

from gor.

It is Interesting. JAVA_OPTS bring new error. Here is the command I used:

export JAVA_OPTS="-Xms2G -Xmx5G"
export MODULEPATH=/share/apps/compute/modulefiles/applications:$MODULEPATH
module load gor
cd /share/apps/compute/gor/
/share/apps/compute/gor/tools/build/install/tools/bin/gorshell
gor /home/sguo2/janssen4/oasis/bin/gor/tests/data/gor/dbsnp_test.gor | top 10 

Here is the error:

(base) [sguo2@comet-ln2 gor]$ export JAVA_OPTS="-Xms2G -Xmx5G"
(base) [sguo2@comet-ln2 gor]$ export MODULEPATH=/share/apps/compute/modulefiles/applications:$MODULEPATH
(base) [sguo2@comet-ln2 gor]$ module load gor
(base) [sguo2@comet-ln2 gor]$ cd /share/apps/compute/gor/
(base) [sguo2@comet-ln2 gor]$ /share/apps/compute/gor/tools/build/install/tools/bin/gorshell
Error occurred during initialization of VM
java.lang.OutOfMemoryError: unable to create new native thread
(base) [sguo2@comet-ln2 gor]$ gor /home/sguo2/janssen4/oasis/bin/gor/tests/data/gor/dbsnp_test.gor | top 10
top: unknown option '1'
Usage:
  top -hv | -bcHiOSs -d secs -n max -u|U user -p pid(s) -o field -w [cols]

from gor.

@Shicheng-Guo there are two issues here:

1. you should not be using the gor command, instead you should be using the gorpipe command.
2. when writing gorpipe commands, you need to quote the gor query to avoid your shell taking over the parsing of the line.

So try something like this:

gorpipe "/home/sguo2/janssen4/oasis/bin/gor/tests/data/gor/dbsnp_test.gor | top 10"

from gor.

@StFS these two reply really helpful!!

I agree with you gorpipe work well and don't affect linux bash. However, the following script works:

gorpipe /home/sguo2/janssen4/oasis/bin/gor/tests/data/gor/dbsnp_test.gor | head

Thanks.

Shicheng

from gor.

@Shicheng-Guo yes, head works because that's a valid Linux command. In that case the gorpipe command is reading and outputting all the rows from the file you're querying but head is simply ignoring everything but the first few lines.

This is inefficient compared to using the GOR top command, as that will allow GOR to stop reading the file once it has read the number of rows requested.

from gor.